Package: bamsignals 1.37.0

Johannes Helmuth

bamsignals: Extract read count signals from bam files

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

Authors:Alessandro Mammana [aut, cre], Johannes Helmuth [aut]

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bamsignals/json (API)
NEWS

# Install 'bamsignals' in R:

install.packages('bamsignals', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lamortenera/bamsignals/issues

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library
c++– GNU Standard C++ Library v3

On BioConductor:bamsignals-1.37.0(bioc 3.20)bamsignals-1.36.0(bioc 3.19)

bioconductor-package

6 exports 2.83 score 19 dependencies 12 dependents 5 mentions

Last updated 2 months agofrom:92298a4cdf

Exports:alignSignals as.list bamCount bamCoverage bamProfile width

Dependencies:askpass BiocGenerics curl GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite mime openssl R6 Rcpp Rhtslib S4Vectors sys UCSC.utils XVector zlibbioc

Introduction to the bamsignals package

Alessandro Mammana and Johannes Helmuth

Rendered frombamsignals.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2016-04-11
Started: 2015-02-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Converts the container to a list 'l' such that 'l[[i]]' is the i-th signal.	as.list.CountSignals
Efficient counting of reads in a bam file	bamsignals-package bamsignals
Functions for extracting count signals from a bam file.	bamCount bamCount,character,GenomicRanges-method bamCoverage bamCoverage,character,GenomicRanges-method bamProfile bamProfile,character,GenomicRanges-method bamsignals-methods
Container for count signals	alignSignals alignSignals,CountSignals-method as.list as.list,CountSignals-method CountSignals CountSignals-class length length,CountSignals-method width width,CountSignals-method [,CountSignals,ANY-method